Developers of computer software applications may use tools to create models of their applications. Developers may begin developing an application by first creating a model of the application, and then using tools to automatically generate computer software application code from the model. In other instances, such as where developers work with pre-existing legacy application code, developers may use tools to create a model of an application based on the pre-existing code. Unfortunately, not all aspects of the pre-existing code may be reflected in the model. Furthermore, once a model of an application and the application code are in hand, a developer may wish to make changes to the code and have them reflected in the model, and vice versa, yet not all changes that are made to the code may be reflected in the model. Thus, if the model is used to regenerate the code entirely, such as when instrumenting the code to include instructions that are used to monitor the behavior of the application during execution, as well as when removing such instrumentation, any aspects of the code that are not reflected in the model may be overwritten.